Regulation of Alternative Sigma Factor Use

Osterberg, S; Peso-Santos, Teresa del; Shingler, Victoria

doi:10.1146/annurev.micro.112408.134219

Cited by 209 publications

(234 citation statements)

References 88 publications

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“…In turn, the latter can thus associate with the RNA polymerase and can induce expression of its regulon. In this mechanism, the availability of the sigma factor depends on the phosphorylation state of the anti-sigma antagonist (30,31). Although partner-switching systems were initially unveiled in Gram-positive bacteria, they have also been found in some Gram-negative bacteria including Bordetella (BtrWVU), Vibrio fisheri (SypEA), and Pseudomonas aeruginosa (HsbRA).…”

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confidence: 99%

The General Stress Response σS Is Regulated by a Partner Switch in the Gram-negative Bacterium Shewanella oneidensis

Bouillet¹,

Genest²,

Jourlin-Castelli³

et al. 2016

Journal of Biological Chemistry

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Edited by Thomas SöllnerHere, we show that a partner-switching system of the aquatic Proteobacterium Shewanella oneidensis regulates post-translationally S (also called RpoS), the general stress response sigma factor. Genes SO2118 and SO2119 encode CrsA and CrsR, respectively. CrsR is a three-domain protein comprising a receiver, a phosphatase, and a kinase/anti-sigma domains, and CrsA is an anti-sigma antagonist. In vitro, CrsR sequesters S and possesses kinase and phosphatase activities toward CrsA. In turn, dephosphorylated CrsA binds the anti-sigma domain of CrsR to allow the release of S . This study reveals a novel pathway that post-translationally regulates the general stress response sigma factor differently than what was described for other proteobacteria like Escherichia coli. We argue that this pathway allows probably a rapid bacterial adaptation.

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confidence: 99%

The General Stress Response σS Is Regulated by a Partner Switch in the Gram-negative Bacterium Shewanella oneidensis

Bouillet¹,

Genest²,

Jourlin-Castelli³

et al. 2016

Journal of Biological Chemistry

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“…Multiple sigma factors compete for binding to core RNAP (reviewed in refs. 3,4), and each sigma factor controls a specific set of promoters.In Escherichia coli, which has seven sigma factors, σ 70 is the primary sigma, and σ S is important for certain stress responses and during the stationary phase of growth (5). Eσ S -dependent transcription initiation is regulated by σ S , whose concentration is itself regulated at the levels of transcription, translation, and protein stability (reviewed in ref.…”

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confidence: 99%

“…Multiple sigma factors compete for binding to core RNAP (reviewed in refs. 3,4), and each sigma factor controls a specific set of promoters.…”

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confidence: 99%

Key features of σ ^S required for specific recognition by Crl, a transcription factor promoting assembly of RNA polymerase holoenzyme

Banta¹,

Chumanov

Yuan

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Bacteria use multiple sigma factors to coordinate gene expression in response to environmental perturbations. In Escherichia coli and other γ-proteobacteria, the transcription factor Crl stimulates σ Sdependent transcription during times of cellular stress by promoting the association of σ S with core RNA polymerase. The molecular basis for specific recognition of σ S by Crl, rather than the homologous and more abundant primary sigma factor σ 70 , is unknown. Here we use bacterial two-hybrid analysis in vivo and p-benzoylphenylalanine cross-linking in vitro to define the features in σ S responsible for specific recognition by Crl. We identify residues in σ S conserved domain 2 (σ S 2 ) that are necessary and sufficient to allow recognition of σ 70 conserved domain 2 by Crl, one near the promoter-melting region and the other at the position where a large nonconserved region interrupts the sequence of σ 70 . We then use luminescence resonance energy transfer to demonstrate directly that Crl promotes holoenzyme assembly using these specificity determinants on σ S . Our results explain how Crl distinguishes between sigma factors that are largely homologous and activates discrete sets of promoters even though it does not bind to promoter DNA.RNAP formation | transcription initiation | bacterial stress response | RpoS | curli fiber T ranscription initiation in bacteria requires the assembly of a sigma factor (σ) with the RNA polymerase (RNAP) catalytic core (E, composed of 2 α-subunits and one each of β, β′, and ω) to form RNAP holoenzyme (Eσ), which in turn recognizes promoter sequences (1) (reviewed in ref. 2). Multiple sigma factors compete for binding to core RNAP (reviewed in refs. 3,4), and each sigma factor controls a specific set of promoters.In Escherichia coli, which has seven sigma factors, σ 70 is the primary sigma, and σ S is important for certain stress responses and during the stationary phase of growth (5). Eσ S -dependent transcription initiation is regulated by σ S , whose concentration is itself regulated at the levels of transcription, translation, and protein stability (reviewed in ref. 6). Eσ S -dependent transcription is also activated by Crl (7), a small protein that increases expression of many stress response genes and those required for formation of amyloid curli fibers (which accounts for its name) involved in adhesion and biofilm formation (reviewed in refs. 2,6,8).The effect of Crl on σ S -dependent transcription in vivo is most pronounced during the transition into stationary phase (9). It has been proposed that Crl functions by increasing the concentration of Eσ S holoenzyme by facilitating assembly of σ S with core RNAP (10-12) because Crl's effects on transcription are greatest in vitro when the concentration of σ S is lowest, and overexpression of σ S complements a crl deletion in vivo (13). Effects of Crl have also been reported on postholoenzyme assembly steps including promoter binding (14) and open complex formation (12).Sigma factors contain several protease-resistant domains, e...

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“…The activity of anti-sigma factors must itself be regulated, and this is achieved by a variety of mechanisms, such as direct stimulus sensing followed by conformational changes, regulated intramembrane proteolysis by sensor proteases, or partner switches with anti-sigma factor antagonists (6,(8)(9)(10)(11). Although there is considerable understanding of antisigma factor regulation for a few systems, this is not the case for the vast majority of systems.…”

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Structural basis for sigma factor mimicry in the general stress response of Alphaproteobacteria

Campagne

Damberger

Kaczmarczyk³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Reprogramming gene expression is an essential component of adaptation to changing environmental conditions. In bacteria, a widespread mechanism involves alternative sigma factors that redirect transcription toward specific regulons. The activity of sigma factors is often regulated through sequestration by cognate anti-sigma factors; however, for most systems, it is not known how the activity of the anti-sigma factor is controlled to release the sigma factor. Recently, the general stress response sigma factor in Alphaproteobacteria, σ EcfG , was identified. σ EcfG is inactivated by the anti-sigma factor NepR, which is itself regulated by the response regulator PhyR. This key regulator sequesters NepR upon phosphorylation of its PhyR receiver domain via its σ EcfG sigma factor-like output domain (PhyR SL ). To understand the molecular basis of the PhyR-mediated partner-switching mechanism, we solved the structure of the PhyR SL –NepR complex using NMR. The complex reveals an unprecedented anti-sigma factor binding mode: upon PhyR SL binding, NepR forms two helices that extend over the surface of the PhyR SL subdomains. Homology modeling and comparative analysis of NepR, PhyR SL , and σ EcfG mutants indicate that NepR contacts both proteins with the same determinants, showing sigma factor mimicry at the atomic level. A lower density of hydrophobic interactions, together with the absence of specific polar contacts in the σ EcfG –NepR complex model, is consistent with the higher affinity of NepR for PhyR compared with σ EcfG . Finally, by reconstituting the partner switch in vitro, we demonstrate that the difference in affinity of NepR for its partners is sufficient for the switch to occur.

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Regulation of Alternative Sigma Factor Use

Cited by 209 publications

References 88 publications

The General Stress Response σS Is Regulated by a Partner Switch in the Gram-negative Bacterium Shewanella oneidensis

The General Stress Response σS Is Regulated by a Partner Switch in the Gram-negative Bacterium Shewanella oneidensis

Key features of σ ^S required for specific recognition by Crl, a transcription factor promoting assembly of RNA polymerase holoenzyme

Structural basis for sigma factor mimicry in the general stress response of Alphaproteobacteria

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Regulation of Alternative Sigma Factor Use

Cited by 209 publications

References 88 publications

The General Stress Response σS Is Regulated by a Partner Switch in the Gram-negative Bacterium Shewanella oneidensis

The General Stress Response σS Is Regulated by a Partner Switch in the Gram-negative Bacterium Shewanella oneidensis

Key features of σ S required for specific recognition by Crl, a transcription factor promoting assembly of RNA polymerase holoenzyme

Structural basis for sigma factor mimicry in the general stress response of Alphaproteobacteria

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Key features of σ ^S required for specific recognition by Crl, a transcription factor promoting assembly of RNA polymerase holoenzyme